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Self-complementary oligonucleotides were synthesized at atomically-flat Si(111) surfaces and their hybridization reaction was studied using atomic force microscopy. Annealing these surfaces in aqueous media, in the absence of any other reagents or DNA, resulted in a self-organization process in which hybridization produced well-defined features in the AFM images. By varying the surface coverage of DNA we provide evidence that the features observed are due to inter-strand rather than intra-strand hybridization reactions.